well, it is up to you but I find it better to keep each site separate.
Install Geeklog, and put in all your plugins, patches, hacks and upgrades.
Use the installer script to build the MySQL database, html root structures etc. Make sure it works.
Then copy everything - the core files, database and html files.
Give the base directories new meaningful names and edit the config files accordingly. Don't forget to change the SQL user names and permissions.
Each site runs independantly and no worries with cross-contamination of data etc.
Of course the downside is you have to update/upgrade each site individually when the time comes.